Mercurial > repos > yufei-luo > s_mart
view commons/core/sql/TableMapAdaptator.py @ 14:c79b9ae3f65f
Deleted selected files
author | m-zytnicki |
---|---|
date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. import sys from commons.core.sql.TableAdaptator import TableAdaptator from commons.core.sql.ITableMapAdaptator import ITableMapAdaptator from commons.core.coord.Map import Map from commons.core.coord.MapUtils import MapUtils ## Adaptator for Map table # class TableMapAdaptator( TableAdaptator, ITableMapAdaptator ): ## Give a list of Map instances having a given seq name # # @param seqName string seq name # @return lMap list of instances # def getListFromSeqName( self, seqName ): sqlCmd = "SELECT * FROM %s" % (self._table) colum2Get, type2Get, attr2Get = self._getTypeColumAttr2Get(seqName) sqlCmd += " WHERE " + colum2Get sqlCmd += " = " sqlCmd = sqlCmd + type2Get sqlCmd = sqlCmd % "'" + attr2Get + "'" return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) ## Give a list of Map instances overlapping a given region # # @param query string query name # @param start integer start coordinate # @param end integer end coordinate # @return list map instances # def getListOverlappingCoord(self, query, start, end): sqlCmd = 'select * from %s where chr="%s" and ((start between least(%d,%d) and greatest(%d,%d) or end between least(%d,%d) and greatest(%d,%d)) or (least(start,end)<=least(%d,%d) and greatest(start,end)>=greatest(%d,%d))) ;' % (self._table, query, start, end, start, end, start, end, start, end, start, end, start, end) return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) ## Give a list of Map instances having a given sequence name # # @param seqName string sequence name # @return lMap list of instances # def getMapListFromSeqName(self, seqName): lMap = self.getListFromSeqName( seqName ) return lMap #TODO: Check getListFromSeqName method: uses name instead of seqname # ## Give a list of Map instances having a given sequence name from list # # # # @param lSeqName string sequence name list # # @return lMap list of instances # # # def getMapListFromSeqNameList(self, lSeqName): # lMap = [] # [lMap.extend(self.getListFromSeqName(seqName)) for seqName in lSeqName] # return lMap ## Give a list of Map instances having a given chromosome # # @param chr string chromosome # @return lMap list of instances # def getMapListFromChr(self, chr): sqlCmd = "SELECT * FROM %s WHERE chr='%s'" % (self._table, chr) lMap = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lMap ## Give a list of the distinct seqName/chr present in the table # # @return lDistinctContigNames string list # def getSeqNameList(self): sqlCmd = "SELECT DISTINCT chr FROM %s" % ( self._table ) lDistinctContigNames = self._iDb.getStringListWithSQLCmd(sqlCmd) return lDistinctContigNames ## Return a list of Set instances from a given sequence name # # @param seqName string sequence name # @return lSets list of Set instances # def getSetListFromSeqName( self, seqName ): lMaps = self.getListFromSeqName( seqName ) lSets = MapUtils.mapList2SetList( lMaps ) return lSets ## Give a map instances list overlapping a given region # # @param seqName string seq name # @param start integer start coordinate # @param end integer end coordinate # @return lMap list of map instances # def getMapListOverlappingCoord(self, seqName, start, end): lMap = self.getListOverlappingCoord(seqName, start, end) return lMap ## Return a list of Set instances overlapping a given sequence # # @param seqName string sequence name # @param start integer start coordinate # @param end integer end coordinate # @return lSet list of Set instances # def getSetListOverlappingCoord( self, seqName, start, end ): lMaps = self.getListOverlappingCoord( seqName, start, end ) lSets = MapUtils.mapList2SetList( lMaps ) return lSets ## Give a dictionary which keys are Map names and values the corresponding Map instances # # @return dName2Maps dict which keys are Map names and values the corresponding Map instances # def getDictPerName( self ): dName2Maps = {} lMaps = self.getListOfAllMaps() for iMap in lMaps: if dName2Maps.has_key( iMap.name ): if iMap == dName2Maps[ iMap.name ]: continue else: msg = "ERROR: in table '%s' two different Map instances have the same name '%s'" % ( self._table, iMap.name ) sys.stderr.write( "%s\n" % ( msg ) ) sys.exit(1) dName2Maps[ iMap.name ] = iMap return dName2Maps ## Return a list of Map instances with all the data contained in the table # # @return lMaps list of Map instances # def getListOfAllMaps( self ): sqlCmd = "SELECT * FROM %s" % ( self._table ) lMaps = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lMaps ## Give the end of map as integer # # @return end integer the end of map # def getEndFromSeqName(self, seqName): sqlCmd = "SELECT end FROM %s WHERE chr = '%s'" % (self._table, seqName) end = self._iDb.getIntegerWithSQLCmd(sqlCmd) return end def _getInstanceToAdapt(self): iMap = Map() return iMap def _getTypeColumAttr2Get(self, name): colum2Get = 'name' type2Get = '%s' attr2Get = name return colum2Get, type2Get, attr2Get def _getTypeAndAttr2Insert(self, map): type2Insert = ("'%s'","'%s'","'%d'","'%d'") attr2Insert = (map.name, map.seqname, map.start, map.end) return type2Insert, attr2Insert def _escapeAntislash(self, obj): obj.name = obj.name.replace("\\", "\\\\") obj.seqname = obj.seqname.replace("\\", "\\\\")